void Reallocate_Neighbor_List( reax_list *far_nbrs, int n, int num_intrs,
MPI_Comm comm )
{
Delete_List( far_nbrs, comm );
if(!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs, comm )){
fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
/*
* Must be called on the worker that created the bag, no check yet!
*/
static int
p_dbag_dissolve(value vdbag, type tdbag, value vl, type tl)
{
aport_id_t bag_aport_id;
dbag_descr_t *dbag_descr;
amsg_t this_msg;
amsg_ref_t *this_msg_data_hdr;
pword list;
register pword *car, *cdr;
Check_Integer(tdbag);
bag_aport_id = (aport_id_t) vdbag.nint;
Check_Output_List(tl);
if (aport_get_option(bag_aport_id, APORT_DATA_PTR,
(aport_optval_t *) &dbag_descr) != AMSG_OK)
{
Bip_Error(MPS_ERROR);
}
this_msg = dbag_descr->first.msg;
this_msg_data_hdr = dbag_descr->first.msg_data_hdr;
hp_free_size((generic_ptr) dbag_descr, sizeof(dbag_descr_t));
cdr = &list;
while (this_msg_data_hdr != &dbag_descr->first)
{
pword *pw1;
amsg_t old_msg;
car = TG;
Push_List_Frame();
Make_List(cdr, car);
cdr = car + 1;
pw1 = dbformat_to_term((char*)(this_msg_data_hdr+1), D_UNKNOWN, tdict);
if (!pw1)
{
value va;
va.did = d_.abort;
Bip_Throw(va, tdict);
}
car->val.ptr = pw1->val.ptr;
car->tag.kernel = pw1->tag.kernel;
old_msg = this_msg;
this_msg = this_msg_data_hdr->msg;
this_msg_data_hdr = this_msg_data_hdr->msg_data_hdr;
(void) amsg_free(old_msg);
}
Make_Nil(cdr);
if (aport_deallocate(bag_aport_id) != AMSG_OK)
{
Bip_Error(MPS_ERROR);
}
Return_Unify_Pw(vl, tl, list.val, list.tag);
}
int Reallocate_Bonds_List( reax_system *system, reax_list *bonds,
int *total_bonds, int *est_3body, MPI_Comm comm )
{
int i;
*total_bonds = 0;
*est_3body = 0;
for( i = 0; i < system->N; ++i ){
*est_3body += SQR(system->my_atoms[i].num_bonds);
// commented out - already updated in validate_lists in forces.c
// system->my_atoms[i].num_bonds = MAX( Num_Entries(i,bonds)*2, MIN_BONDS );
*total_bonds += system->my_atoms[i].num_bonds;
}
*total_bonds = (int)(MAX( *total_bonds * SAFE_ZONE, MIN_CAP*MIN_BONDS ));
Delete_List( bonds, comm );
if(!Make_List(system->total_cap, *total_bonds, TYP_BOND, bonds, comm)) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
return SUCCESS;
}
int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds,
MPI_Comm comm )
{
int i, id, total_hbonds;
total_hbonds = 0;
for( i = 0; i < system->n; ++i )
if( (id = system->my_atoms[i].Hindex) >= 0 ) {
// commented out - already updated in validate_lists in forces.c
// system->my_atoms[i].num_hbonds = MAX(Num_Entries(id,hbonds)*SAFER_ZONE,
// MIN_HBONDS);
total_hbonds += system->my_atoms[i].num_hbonds;
}
total_hbonds = (int)(MAX( total_hbonds*SAFER_ZONE, MIN_CAP*MIN_HBONDS ));
Delete_List( hbonds, comm );
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND, hbonds, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
return total_hbonds;
}
void ReAllocate( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data )
{
int i, j, k, p;
int num_bonds, est_3body, nflag, Nflag, Hflag, mpi_flag, ret, total_send;
int renbr, newsize;
reallocate_data *realloc;
reax_list *far_nbrs;
sparse_matrix *H;
grid *g;
neighbor_proc *nbr_pr;
mpi_out_data *nbr_data;
MPI_Comm comm;
char msg[200];
realloc = &(workspace->realloc);
g = &(system->my_grid);
comm = mpi_data->world;
#if defined(DEBUG)
fprintf( stderr, "p%d@reallocate: n: %d, N: %d, numH: %d\n",
system->my_rank, system->n, system->N, system->numH );
fprintf( stderr, "p%d@reallocate: local_cap: %d, total_cap: %d, Hcap: %d\n",
system->my_rank, system->local_cap, system->total_cap,
system->Hcap);
fprintf( stderr, "p%d: realloc.num_far: %d\n",
system->my_rank, realloc->num_far );
fprintf( stderr, "p%d: realloc.H: %d, realloc.Htop: %d\n",
system->my_rank, realloc->H, realloc->Htop );
fprintf( stderr, "p%d: realloc.Hbonds: %d, realloc.num_hbonds: %d\n",
system->my_rank, realloc->hbonds, realloc->num_hbonds );
fprintf( stderr, "p%d: realloc.bonds: %d, num_bonds: %d\n",
system->my_rank, realloc->bonds, realloc->num_bonds );
fprintf( stderr, "p%d: realloc.num_3body: %d\n",
system->my_rank, realloc->num_3body );
#endif
// IMPORTANT: LOOSE ZONES CHECKS ARE DISABLED FOR NOW BY &&'ing with 0!!!
nflag = 0;
if( system->n >= DANGER_ZONE * system->local_cap ||
(0 && system->n <= LOOSE_ZONE * system->local_cap) ) {
nflag = 1;
system->local_cap = MAX( (int)(system->n * SAFE_ZONE), MIN_CAP );
}
Nflag = 0;
if( system->N >= DANGER_ZONE * system->total_cap ||
(0 && system->N <= LOOSE_ZONE * system->total_cap) ) {
Nflag = 1;
system->total_cap = MAX( (int)(system->N * SAFE_ZONE), MIN_CAP );
}
if( Nflag ) {
/* system */
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating system and workspace -"\
"n=%d N=%d local_cap=%d total_cap=%d\n",
system->my_rank, system->n, system->N,
system->local_cap, system->total_cap );
#endif
ret = Allocate_System( system, system->local_cap, system->total_cap, msg );
if( ret != SUCCESS ) {
fprintf( stderr, "not enough space for atom_list: total_cap=%d",
system->total_cap );
fprintf( stderr, "terminating...\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
/* workspace */
DeAllocate_Workspace( control, workspace );
ret = Allocate_Workspace( system, control, workspace, system->local_cap,
system->total_cap, comm, msg );
if( ret != SUCCESS ) {
fprintf( stderr, "no space for workspace: local_cap=%d total_cap=%d",
system->local_cap, system->total_cap );
fprintf( stderr, "terminating...\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
renbr = (data->step - data->prev_steps) % control->reneighbor == 0;
/* far neighbors */
if( renbr ) {
far_nbrs = *lists + FAR_NBRS;
if( Nflag || realloc->num_far >= far_nbrs->num_intrs * DANGER_ZONE ) {
if( realloc->num_far > far_nbrs->num_intrs ) {
fprintf( stderr, "step%d-ran out of space on far_nbrs: top=%d, max=%d",
data->step, realloc->num_far, far_nbrs->num_intrs );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
newsize = static_cast<int>
(MAX( realloc->num_far*SAFE_ZONE, MIN_CAP*MIN_NBRS ));
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating far_nbrs: num_fars=%d, space=%dMB\n",
system->my_rank, (int)(realloc->num_far*SAFE_ZONE),
(newsize*sizeof(far_neighbor_data)/(1024*1024)) );
#endif
Reallocate_Neighbor_List( far_nbrs, system->total_cap, newsize, comm );
realloc->num_far = 0;
}
}
#if defined(PURE_REAX)
/* qeq coef matrix */
H = workspace->H;
if( nflag || realloc->Htop >= H->m * DANGER_ZONE ) {
if( realloc->Htop > H->m ) {
fprintf( stderr,
"step%d - ran out of space on H matrix: Htop=%d, max = %d",
data->step, realloc->Htop, H->m );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating H matrix: Htop=%d, space=%dMB\n",
system->my_rank, (int)(realloc->Htop*SAFE_ZONE),
(int)(realloc->Htop * SAFE_ZONE * sizeof(sparse_matrix_entry) /
(1024*1024)) );
#endif
newsize = static_cast<int>
(MAX( realloc->Htop*SAFE_ZONE, MIN_CAP*MIN_NBRS ));
Reallocate_Matrix( &(workspace->H), system->local_cap,
newsize, "H", comm );
//Deallocate_Matrix( workspace->L );
//Deallocate_Matrix( workspace->U );
workspace->L = NULL;
workspace->U = NULL;
realloc->Htop = 0;
}
#endif /*PURE_REAX*/
/* hydrogen bonds list */
if( control->hbond_cut > 0 ) {
Hflag = 0;
if( system->numH >= DANGER_ZONE * system->Hcap ||
(0 && system->numH <= LOOSE_ZONE * system->Hcap) ) {
Hflag = 1;
system->Hcap = MAX( system->numH * SAFER_ZONE, MIN_CAP );
}
if( Hflag || realloc->hbonds ) {
ret = Reallocate_HBonds_List( system, (*lists)+HBONDS, comm );
realloc->hbonds = 0;
#if defined(DEBUG_FOCUS)
fprintf(stderr, "p%d: reallocating hbonds: total_hbonds=%d space=%dMB\n",
system->my_rank, ret, (int)(ret*sizeof(hbond_data)/(1024*1024)));
#endif
}
}
/* bonds list */
num_bonds = est_3body = -1;
if( Nflag || realloc->bonds ){
Reallocate_Bonds_List( system, (*lists)+BONDS, &num_bonds,
&est_3body, comm );
realloc->bonds = 0;
realloc->num_3body = MAX( realloc->num_3body, est_3body );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating bonds: total_bonds=%d, space=%dMB\n",
system->my_rank, num_bonds,
(int)(num_bonds*sizeof(bond_data)/(1024*1024)) );
#endif
}
/* 3-body list */
if( realloc->num_3body > 0 ) {
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating 3body list: num_3body=%d, space=%dMB\n",
system->my_rank, realloc->num_3body,
(int)(realloc->num_3body * sizeof(three_body_interaction_data) /
(1024*1024)) );
#endif
Delete_List( (*lists)+THREE_BODIES, comm );
if( num_bonds == -1 )
num_bonds = ((*lists)+BONDS)->num_intrs;
realloc->num_3body = (int)(MAX(realloc->num_3body*SAFE_ZONE, MIN_3BODIES));
if( !Make_List( num_bonds, realloc->num_3body, TYP_THREE_BODY,
(*lists)+THREE_BODIES, comm ) ) {
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, CANNOT_INITIALIZE );
}
realloc->num_3body = -1;
}
#if defined(PURE_REAX)
/* grid */
if( renbr && realloc->gcell_atoms > -1 ) {
#if defined(DEBUG_FOCUS)
fprintf(stderr, "reallocating gcell: g->max_atoms: %d\n", g->max_atoms);
#endif
for( i = g->native_str[0]; i < g->native_end[0]; i++ )
for( j = g->native_str[1]; j < g->native_end[1]; j++ )
for( k = g->native_str[2]; k < g->native_end[2]; k++ ) {
// reallocate g->atoms
sfree( g->cells[i][j][k].atoms, "g:atoms" );
g->cells[i][j][k].atoms = (int*)
scalloc( realloc->gcell_atoms, sizeof(int), "g:atoms", comm);
}
realloc->gcell_atoms = -1;
}
/* mpi buffers */
// we have to be at a renbring step -
// to ensure correct values at mpi_buffers for update_boundary_positions
if( !renbr )
mpi_flag = 0;
// check whether in_buffer capacity is enough
else if( system->max_recved >= system->est_recv * 0.90 )
mpi_flag = 1;
else {
// otherwise check individual outgoing buffers
mpi_flag = 0;
for( p = 0; p < MAX_NBRS; ++p ) {
nbr_pr = &( system->my_nbrs[p] );
nbr_data = &( mpi_data->out_buffers[p] );
if( nbr_data->cnt >= nbr_pr->est_send * 0.90 ) {
mpi_flag = 1;
break;
}
}
}
if( mpi_flag ) {
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating mpi_buf: old_recv=%d\n",
system->my_rank, system->est_recv );
for( p = 0; p < MAX_NBRS; ++p )
fprintf( stderr, "p%d: nbr%d old_send=%d\n",
system->my_rank, p, system->my_nbrs[p].est_send );
#endif
/* update mpi buffer estimates based on last comm */
system->est_recv = MAX( system->max_recved*SAFER_ZONE, MIN_SEND );
system->est_trans =
(system->est_recv * sizeof(boundary_atom)) / sizeof(mpi_atom);
total_send = 0;
for( p = 0; p < MAX_NBRS; ++p ) {
nbr_pr = &( system->my_nbrs[p] );
nbr_data = &( mpi_data->out_buffers[p] );
nbr_pr->est_send = MAX( nbr_data->cnt*SAFER_ZONE, MIN_SEND );
total_send += nbr_pr->est_send;
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating mpi_buf: recv=%d send=%d total=%dMB\n",
system->my_rank, system->est_recv, total_send,
(int)((system->est_recv+total_send)*sizeof(boundary_atom)/
(1024*1024)));
for( p = 0; p < MAX_NBRS; ++p )
fprintf( stderr, "p%d: nbr%d new_send=%d\n",
system->my_rank, p, system->my_nbrs[p].est_send );
#endif
/* reallocate mpi buffers */
Deallocate_MPI_Buffers( mpi_data );
ret = Allocate_MPI_Buffers( mpi_data, system->est_recv,
system->my_nbrs, msg );
if( ret != SUCCESS ) {
fprintf( stderr, "%s", msg );
fprintf( stderr, "terminating...\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
#endif /*PURE_REAX*/
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: reallocate done\n",
system->my_rank, data->step );
MPI_Barrier( comm );
#endif
}
int Init_Lists( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data, char *msg )
{
int i, num_nbrs;
int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
int nrecv[MAX_NBRS];
MPI_Comm comm;
comm = mpi_data->world;
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
&Htop, hb_top, bond_top, &num_3body, comm );
if( control->hbond_cut > 0 ) {
/* init H indexes */
total_hbonds = 0;
for( i = 0; i < system->n; ++i ) {
system->my_atoms[i].num_hbonds = hb_top[i];
total_hbonds += hb_top[i];
}
total_hbonds = (int)(MAX( total_hbonds*SAFER_ZONE, MIN_CAP*MIN_HBONDS ));
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
*lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
system->my_rank, total_hbonds,
(int)(total_hbonds*sizeof(hbond_data)/(1024*1024)) );
#endif
}
/* bonds list */
//Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
//num_bonds = bond_top[system->N-1];
total_bonds = 0;
for( i = 0; i < system->N; ++i ) {
system->my_atoms[i].num_bonds = bond_top[i];
total_bonds += bond_top[i];
}
bond_cap = (int)(MAX( total_bonds*SAFE_ZONE, MIN_CAP*MIN_BONDS ));
if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
*lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
system->my_rank, bond_cap,
(int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
#endif
/* 3bodies list */
cap_3body = (int)(MAX( num_3body*SAFE_ZONE, MIN_3BODIES ));
if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
*lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
system->my_rank, cap_3body,
(int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
#endif
#if defined(TEST_FORCES)
if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
*lists+DDELTAS, comm ) ) {
fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
system->my_rank, bond_cap*30,
bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
if( !Make_List( bond_cap, bond_cap*50, TYP_DBO, (*lists)+DBOS, comm ) ) {
fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
system->my_rank, bond_cap*MAX_BONDS*3,
bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
#endif
free( hb_top );
free( bond_top );
return SUCCESS;
}
int Init_Lists( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data, char *msg )
{
int i, num_nbrs;
int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
MPI_Comm comm;
comm = mpi_data->world;
//for( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = system->my_nbrs[i].est_recv;
//system->N = SendRecv( system, mpi_data, mpi_data->boundary_atom_type, nrecv,
// Sort_Boundary_Atoms, Unpack_Exchange_Message, 1 );
num_nbrs = Estimate_NumNeighbors( system, lists );
if(!Make_List( system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
*lists+FAR_NBRS, comm )){
fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated far_nbrs: num_far=%d, space=%dMB\n",
system->my_rank, num_nbrs,
(int)(num_nbrs*sizeof(far_neighbor_data)/(1024*1024)) );
#endif
Generate_Neighbor_Lists( system, data, workspace, lists );
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
&Htop, hb_top, bond_top, &num_3body, comm );
Allocate_Matrix( &(workspace->H), system->local_cap, Htop, comm );
workspace->L = NULL;
workspace->U = NULL;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated H matrix: Htop=%d, space=%dMB\n",
system->my_rank, Htop,
(int)(Htop * sizeof(sparse_matrix_entry) / (1024*1024)) );
#endif
if( control->hbond_cut > 0 ) {
/* init H indexes */
total_hbonds = 0;
for( i = 0; i < system->n; ++i ) {
system->my_atoms[i].num_hbonds = hb_top[i];
total_hbonds += hb_top[i];
}
total_hbonds = MAX( total_hbonds*SAFER_ZONE, MIN_CAP*MIN_HBONDS );
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
*lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
system->my_rank, total_hbonds,
(int)(total_hbonds*sizeof(hbond_data)/(1024*1024)) );
#endif
}
/* bonds list */
//Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
//num_bonds = bond_top[system->N-1];
total_bonds = 0;
for( i = 0; i < system->N; ++i ) {
system->my_atoms[i].num_bonds = bond_top[i];
total_bonds += bond_top[i];
}
bond_cap = MAX( total_bonds*SAFE_ZONE, MIN_CAP*MIN_BONDS );
if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
*lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
system->my_rank, bond_cap,
(int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
#endif
/* 3bodies list */
cap_3body = MAX( num_3body*SAFE_ZONE, MIN_3BODIES );
if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
*lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
system->my_rank, cap_3body,
(int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
#endif
#if defined(TEST_FORCES)
if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
*lists+DDELTAS, comm ) ) {
fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
system->my_rank, bond_cap*30,
bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
if( !Make_List( bond_cap, bond_cap*50, TYP_DBO, *lists+DBOS, comm ) ) {
fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
system->my_rank, bond_cap*MAX_BONDS*3,
bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
#endif
free( hb_top );
free( bond_top );
return SUCCESS;
}
int Init_ListsOMP( reax_system *system, control_params *control,
simulation_data * /* data */, storage * /* workspace */,
reax_list **lists, mpi_datatypes *mpi_data, char * /* msg */)
{
int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
MPI_Comm comm;
int mincap = system->mincap;
double safezone = system->safezone;
double saferzone = system->saferzone;
comm = mpi_data->world;
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
&Htop, hb_top, bond_top, &num_3body, comm );
if (control->hbond_cut > 0) {
/* init H indexes */
total_hbonds = 0;
for( i = 0; i < system->n; ++i ) {
system->my_atoms[i].num_hbonds = hb_top[i];
total_hbonds += hb_top[i];
}
total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS ));
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
*lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
total_bonds = 0;
for( i = 0; i < system->N; ++i ) {
system->my_atoms[i].num_bonds = bond_top[i];
total_bonds += bond_top[i];
}
bond_cap = (int)(MAX( total_bonds*safezone, mincap*MIN_BONDS ));
if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
*lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
int nthreads = control->nthreads;
reax_list *bonds = (*lists)+BONDS;
for (i = 0; i < bonds->num_intrs; ++i)
bonds->select.bond_list[i].bo_data.CdboReduction =
(double*) smalloc(sizeof(double)*nthreads, "CdboReduction", comm);
/* 3bodies list */
cap_3body = (int)(MAX( num_3body*safezone, MIN_3BODIES ));
if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
*lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
free( hb_top );
free( bond_top );
return SUCCESS;
}
